Package Bio :: Package Clustalw
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Package Clustalw

source code

A set of classes to interact with the multiple alignment command line program clustalw.

Clustalw is the command line version of the graphical Clustalx aligment program.

This requires clustalw available from:

ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/.

functions: o read o parse_file o do_alignment

classes: o ClustalAlignment o MultipleAlignCL

Classes [hide private]
  ClustalAlignment
Work with the clustal aligment format.
  MultipleAlignCL
Represent a clustalw multiple alignment command line.
Functions [hide private]
 
parse_file(file_name, alphabet=IUPACUnambiguousDNA(), debug_level=0)
Parse the given file into a clustal aligment object.
source code
 
do_alignment(command_line, alphabet=None)
Perform an alignment with the given command line.
source code
Function Details [hide private]

parse_file(file_name, alphabet=IUPACUnambiguousDNA(), debug_level=0)

source code 

Parse the given file into a clustal aligment object.

Arguments: o file_name - The name of the file to parse. o alphabet - The type of alphabet to use for the alignment sequences. This should correspond to the type of information contained in the file. Defaults to be unambiguous_dna sequence.

There is a deprecated optional argument debug_level which has no effect.

do_alignment(command_line, alphabet=None)

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Perform an alignment with the given command line.

Arguments: o command_line - A command line object that can give out the command line we will input into clustalw. o alphabet - the alphabet to use in the created alignment. If not specified IUPAC.unambiguous_dna and IUPAC.protein will be used for dna and protein alignment respectively.

Returns: o A clustal alignment object corresponding to the created alignment. If the alignment type was not a clustal object, None is returned.